Contacts of the strand formed by residues 67 - 72 (chain A) in PDB entry 5K26
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A VAL* 3.7 25.2 - - + +
46A TRP 3.4 4.0 - - - -
47A THR* 4.2 15.4 + - + +
65A GLY 3.4 7.1 + - - +
66A ASP* 1.3 72.8 - - - +
68A VAL* 1.3 60.2 + - - +
87A GLN 4.1 2.8 - - - +
88A VAL* 3.7 18.2 - - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 3.3 3.8 - - - -
46A TRP* 2.8 42.0 + - - +
48A ALA 4.6 1.6 - - - +
60A LEU* 4.4 3.1 - - + -
62A LEU* 3.8 17.5 - - + -
66A ASP* 3.9 12.6 - - + +
67A ARG* 1.3 75.9 - - - +
69A GLU* 1.3 70.9 + - - +
70A VAL* 3.4 5.3 + - + +
86A GLY* 4.2 4.0 - - - -
87A GLN 3.7 4.5 - - - +
88A VAL* 3.6 21.5 - - + -
95A PHE* 3.8 31.2 - - + -
100A VAL* 4.3 14.8 - - + -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 4.5 6.3 - - - +
43A ASN* 2.8 55.5 + - + +
44A PRO 3.6 3.6 - - - -
45A VAL* 4.3 11.6 - - + +
67A ARG 4.2 0.8 + - - -
68A VAL* 1.3 69.2 - - - +
70A VAL* 1.3 59.6 + - - +
71A LEU* 3.5 10.8 + - + +
86A GLY* 3.1 4.3 - - - -
87A GLN* 2.8 57.8 + - + +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASN* 3.4 18.2 - - - +
44A PRO* 2.9 23.1 + - + +
46A TRP* 3.5 33.0 - - + +
68A VAL* 3.8 7.4 - - + +
69A GLU* 1.3 72.1 - - - +
71A LEU* 1.3 63.2 + - - +
72A SER* 4.0 7.4 - - - +
73A ARG* 3.7 33.7 - - + -
84A TRP* 4.2 8.7 - - + -
85A ALA 3.7 9.2 - - - +
86A GLY* 4.4 0.2 - - - -
95A PHE* 4.0 21.5 - - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ASN* 3.6 33.0 - - - +
69A GLU* 4.1 21.1 - - + +
70A VAL* 1.3 75.0 - - - +
72A SER* 1.3 59.7 + - - +
85A ALA* 2.8 19.9 + - + +
86A GLY* 4.4 4.9 - - - +
87A GLN* 4.4 10.8 - - - +
92A VAL* 4.0 37.2 - - + -
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.6 1.5 - - - -
71A LEU* 1.3 82.0 - - - +
73A ARG* 1.3 64.3 + - - +
74A ASP* 3.1 26.7 + - - +
84A TRP* 3.5 6.1 - - - +
85A ALA* 2.9 38.2 + - - +
201A MES 5.2 3.1 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il